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Contrast Enhancement

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Elizabeth Frink

Contrast Enhancement

I am having some conflicts with the "Enhance Contrast" command in ImageJ and would like to know if anyone has insight into the two problems I am experiencing. I have written a simple macro to run thru a series of tiff images and enhance the contrast using normalization and then save each image as a jpeg. My two problems are as follows:
1) The macro saves each image successfully as a jpeg but when I go back and open them, only a few of them actually had the contrast enhanced, and some only had the contrast enhanced in a portion of the image down to a vertical line thru the image.
2) If I open one of the images in LabVIEW (one that was successfully enhanced in ImageJ), the image appears nearly inverted in greyscale, but not completely because if I invert the image greyscale, it still does not look correct.
Has anyone seen anything like this or have any ideas how to resolve either of these problems?

Thanks!
-Liz

dscho

Re: Contrast Enhancement

Hi,

On Thu, 22 Jul 2010, Elizabeth Frink wrote:

> I am having some conflicts with the "Enhance Contrast" command in ImageJ
> and would like to know if anyone has insight into the two problems I am
> experiencing. I have written a simple macro to run thru a series of tiff
> images and enhance the contrast using normalization and then save each
> image as a jpeg. My two problems are as follows:
>
> 1) The macro saves each image successfully as a jpeg but when I go back
> and open them, only a few of them actually had the contrast enhanced,
> and some only had the contrast enhanced in a portion of the image
> down to a vertical line thru the image.
>
> 2) If I open one of the images in LabVIEW (one that was successfully
> enhanced in ImageJ), the image appears nearly inverted in greyscale,
> but not completely because if I invert the image greyscale, it still
> does not look correct.

> Has anyone seen anything like this or have any ideas how to resolve
> either of these problems?

Can you show your macro?

Ciao,
Johannes

Elizabeth Frink

Re: Contrast Enhancement

Below is my macro (I have shortened the first two lines by replacing a portion of the directory with "..." for illustration purposes only)

sourcedir = "C:\\Users\\Liz\\Documents\\...\\Brightfield\\1st Tear\\";
outdir = "C:\\Users\\Liz\\Documents\\...\\EnhCont\\1st Tear\\";
img = "sam6close_tear_00001-brightfield.tif";
numimg = 240;
start = 1;

for (i=0; i<numimg; i++) {

imnum = start + i;
strimnum = toString(imnum);
inimg = substring(img,0,(lengthOf(img)-(16+lengthOf(strimnum)))) +strimnum + "-brightfield.tif";
infile = sourcedir + inimg;
open(infile);
run("Enhance Contrast", "saturated=0.4");
imgname = substring(inimg,0,(lengthOf(inimg)-16)) + "-contrast.jpg";
outfile = outdir + imgname;
saveAs("Jpeg", outfile);
close();
}

Thanks!
-Liz

From: "Johannes Schindelin" <[hidden email]>
To: "Elizabeth Frink" <[hidden email]>
Cc: [hidden email]
Sent: Friday, July 23, 2010 5:16:04 AM
Subject: Re: Contrast Enhancement

Hi,

On Thu, 22 Jul 2010, Elizabeth Frink wrote:

> Has anyone seen anything like this or have any ideas how to resolve
> either of these problems?

Can you show your macro?

Ciao,
Johannes

Andrew Kligerman

Re: Contrast Enhancement

We use this script to count particles in a stack and use enhance
contrast in the stack. See if this may help.
Andy Kligerman
US EPA

run("Image Sequence...", "open=F:\\runtest\\1.tif number=5 starting=1
increment=1 scale=100 file=");
run("RGB Split");
run("Close");
run("Close");
run("Median...", "radius=3 stack");
for (slice=1; slice<=nSlices; slice++) {run("Set Slice...",
"slice="+slice);
run("Enhance Contrast", "saturated=0.3 normalize ");}
setThreshold(0, 142);
run("Convert to Mask", "stack");
run("Options...", "iterations=3 count=1 edm=Overwrite do=nothing
stack");
run("Fill Holes", "stack");
run("Open","stack");
run("Watershed","stack");
run("Analyze Particles...", "size=250-Infinity circularity=0.75-1.00
show=Masks display exclude clear summarize stack");

run("Stack to Images");

Joachim Wesner

Antwort: Contrast Enhancement

In reply to this post by Elizabeth Frink

ImageJ Interest Group <[hidden email]> schrieb am 22.07.2010 23:50:21:

> 1) The macro saves each image successfully as a jpeg but when I go
> back and open them, only a few of them actually had the contrast
> enhanced, and some only had the contrast enhanced in a portion of
> the image down to a vertical line thru the image.
>
> 2) ...................
>
> Has anyone seen anything like this or have any ideas how to resolve
> either of these problems?

I see no particular problem with your script, however, your description of
1) seems
to indicate that the enhanced file is somehow written **before** the
process is finished.

No idea, if this should/can happen with the "run" command, but for a quick
test, can you add

wait(2000) (or a similar value)

below the run command and see if anything changes?

WRT your 2), no idea, seems to be an incompatible format!?

Sincerely

Joachim

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dscho

Re: Contrast Enhancement

In reply to this post by Elizabeth Frink

Hi,

On Fri, 23 Jul 2010, Elizabeth Frink wrote:

> Below is my macro (I have shortened the first two lines by replacing a
> portion of the directory with "..." for illustration purposes only)
>
>
> sourcedir = "C:\\Users\\Liz\\Documents\\...\\Brightfield\\1st Tear\\";
> outdir = "C:\\Users\\Liz\\Documents\\...\\EnhCont\\1st Tear\\";
> img = "sam6close_tear_00001-brightfield.tif";
> numimg = 240;
> start = 1;
>
>
> for (i=0; i<numimg; i++) {
>
> imnum = start + i;
> strimnum = toString(imnum);
> inimg = substring(img,0,(lengthOf(img)-(16+lengthOf(strimnum)))) +strimnum + "-brightfield.tif";
> infile = sourcedir + inimg;
> open(infile);
> run("Enhance Contrast", "saturated=0.4");
> imgname = substring(inimg,0,(lengthOf(inimg)-16)) + "-contrast.jpg";
> outfile = outdir + imgname;
> saveAs("Jpeg", outfile);
> close();
> }

Thanks.

I could imagine that there is a timing problem, which you can work around
by calling setBatchMode(true); at the start of the macro (and you can turn
it off at the end with setBatchMode(false);).

Ciao,
Johannes

Elizabeth Frink

Re: Contrast Enhancement

Thanks Johannes (and everyone else) for your suggestions!

The setBatchMode command solved the problem with incomplete and partial contrast enhancements. I will see if I can find some sort of incompatibility issue with LabVIEW and the ImageJ images I have created, with regard to my second conflict.

-Liz

From: "Johannes Schindelin" <[hidden email]>
To: "Elizabeth Frink" <[hidden email]>
Cc: [hidden email]
Sent: Friday, July 23, 2010 10:25:27 AM
Subject: Re: Contrast Enhancement

Hi,

On Fri, 23 Jul 2010, Elizabeth Frink wrote:

Michael Schmid

Re: Contrast Enhancement

Hi Liz,

to me it looks like a race condition in ImageProcessor.createImage,
which is used for saving a JPEG image.
To understand the problem, some more information is needed:

- Image type: 8, 16 or 32(float) bits?
- Java 1.5 or 1.6?
- Which operating system?

Michael
________________________________________________________________

On 23 Jul 2010, at 18:14, Elizabeth Frink wrote:

> Thanks Johannes (and everyone else) for your suggestions!
>
>
> The setBatchMode command solved the problem with incomplete and
> partial contrast enhancements. I will see if I can find some sort
> of incompatibility issue with LabVIEW and the ImageJ images I have
> created, with regard to my second conflict.
>
>
> -Liz
>
>
> From: "Johannes Schindelin" <[hidden email]>
> To: "Elizabeth Frink" <[hidden email]>
> Cc: [hidden email]
> Sent: Friday, July 23, 2010 10:25:27 AM
> Subject: Re: Contrast Enhancement
>
> Hi,
>
> On Fri, 23 Jul 2010, Elizabeth Frink wrote:
>
>> Below is my macro (I have shortened the first two lines by
>> replacing a
>> portion of the directory with "..." for illustration purposes only)
>>
>>
>> sourcedir = "C:\\Users\\Liz\\Documents\\...\\Brightfield\\1st Tear\
>> \";
>> outdir = "C:\\Users\\Liz\\Documents\\...\\EnhCont\\1st Tear\\";
>> img = "sam6close_tear_00001-brightfield.tif";
>> numimg = 240;
>> start = 1;
>>
>>
>> for (i=0; i<numimg; i++) {
>>
>> imnum = start + i;
>> strimnum = toString(imnum);
>> inimg = substring(img,0,(lengthOf(img)-(16+lengthOf(strimnum))))
>> +strimnum + "-brightfield.tif";
>> infile = sourcedir + inimg;
>> open(infile);
>> run("Enhance Contrast", "saturated=0.4");
>> imgname = substring(inimg,0,(lengthOf(inimg)-16)) + "-contrast.jpg";
>> outfile = outdir + imgname;
>> saveAs("Jpeg", outfile);
>> close();
>> }
>
> Thanks.
>
> I could imagine that there is a timing problem, which you can work
> around
> by calling setBatchMode(true); at the start of the macro (and you
> can turn
> it off at the end with setBatchMode(false);).
>
> Ciao,
> Johannes

Elizabeth Frink

Re: Contrast Enhancement

Michael,

The images are 16-bit, it is Java 1.6 and Windows Vista. I think I found the problem yesterday however - I was using images that I had divided by a 48-bit RGB instead of the 16-bit version of the same image. LabVIEW and ImageJ seem to be agreeing with each other much better now.

Thanks!
-Liz

Liz Frink
Laboratory Supervisor
Graduate Research Assistant
Graduate Nuclear or Mechanical Engineering Students (GNOMES) President
Mechanical Testing and Evaluation Laboratory
Mechanical Engineering - Kansas State University
[hidden email]

From: "Michael Schmid" <[hidden email]>
To: [hidden email]
Sent: Tuesday, July 27, 2010 4:27:18 AM
Subject: Re: Contrast Enhancement

Hi Liz,

to me it looks like a race condition in ImageProcessor.createImage,
which is used for saving a JPEG image.
To understand the problem, some more information is needed:

- Image type: 8, 16 or 32(float) bits?
- Java 1.5 or 1.6?
- Which operating system?

Michael
________________________________________________________________

On 23 Jul 2010, at 18:14, Elizabeth Frink wrote: